One thing I am thinking about was raised by Klaxon in the game Saturday Night. This is a different form of play for later in the war - wolfpacks. What I am thinking is a natural evolution - each PC would be a Commanding Officer or an Executive Officer. The CO and XO would split the Approach and Assistant Approach Officer duties between them, with everything else run as defaults - a standard +3 skill level.
The US didn't use wolfpacks until late in the war - 1944 and 1945, but that is time for quite a few patrols. They were generally made up of usually 3-4 subs - though there was at least one 6 sub wolf pack I know about. This would nicely cover a standard PC party, with NPCs to fill in the cracks if needed. In effect, the subs could be operated like fighters, cooperating on hunting down convoys and Japanese naval task forces.
What do you guys think?